Algorithms

Global copy number profiling of cancer genomes.

UNLABELLED: In this article, we introduce a robust and efficient strategy for deriving global and allele-specific copy number alternations (CNA) from cancer whole exome sequencing data based on Log R ratios and B-allele frequencies. Applying the …

Complementary ensemble clustering of biomedical data.

The rapidly growing availability of electronic biomedical data has increased the need for innovative data mining methods. Clustering in particular has been an active area of research in many different application areas, with existing clustering …

Finding and accessing diagrams in biomedical publications.

Complex relationships in biomedical publications are often communicated by diagrams such as bar and line charts, which are a very effective way of summarizing and communicating multi-faceted data sets. Given the ever-increasing amount of published …

Melanoma prognostic model using tissue microarrays and genetic algorithms.

PURPOSE: As a result of the questionable risk-to-benefit ratio of adjuvant therapies, stage II melanoma is currently managed by observation because available clinicopathologic parameters cannot identify the 20% to 60% of such patients likely to …

MEDME: an experimental and analytical methodology for the estimation of DNA methylation levels based on microarray derived MeDIP-enrichment.

DNA methylation is an important component of epigenetic modifications that influences the transcriptional machinery and is aberrant in many human diseases. Several methods have been developed to map DNA methylation for either limited regions or …

Yale Image Finder (YIF): a new search engine for retrieving biomedical images.

UNLABELLED: Yale Image Finder (YIF) is a publicly accessible search engine featuring a new way of retrieving biomedical images and associated papers based on the text carried inside the images. Image queries can also be issued against the image …

Shallow semantic parsing of randomized controlled trial reports.

In this work, we are measuring the performance of Propbank-based Machine Learning (ML) for automatically annotating abstracts of Randomized Controlled Trials (CTRs) with semantically meaningful tags. Propbank is a resource of annotated sentences from …

Term identification in the biomedical literature.

Sophisticated information technologies are needed for effective data acquisition and integration from a growing body of the biomedical literature. Successful term identification is key to getting access to the stored literature information, as it is …

Molecular triangulation: bridging linkage and molecular-network information for identifying candidate genes in Alzheimer's disease.

A major challenge in human genetics is identifying the molecular basis of common heritable disorders. In contrast to rare single-gene diseases, multifactorial disorders are thought to arise from the combined effect of multiple gene variants, such …

Probabilistic inference of molecular networks from noisy data sources.

Information on molecular networks, such as networks of interacting proteins, comes from diverse sources that contain remarkable differences in distribution and quantity of errors. Here, we introduce a probabilistic model useful for predicting protein …